PDB-9dy7: Proteus vulgaris tryptophan indole-lyase complexed with L-ethioni...

ID or keywords:

Entry

Database: PDB / ID: 9dy7

Title

Proteus vulgaris tryptophan indole-lyase complexed with L-ethionine and Na+

Components

Tryptophanase
Tryptophanase (with internal aldimine)

Keywords

LYASE / pyridoxal-5'-phosphate / aminotransferase fold / cation activation / inhibitor complex

Function / homology

Function and homology information

tryptophanase activity / tryptophanase
Similarity search - Function

Biological species

Proteus vulgaris (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.87 Å

Authors

Phillips, R.S.

Funding support

United States, 1items

Citation

Journal: Arch.Biochem.Biophys. / Year: 2025
Title: Structure and dynamics of Proteus vulgaris tryptophan indole-lyase complexes with l-ethionine and l-alanine.
Authors: Phillips, R.S. / Brown, S.M.

History

Deposition	Oct 13, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9dy7.cif.gz	951.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9dy7.ent.gz	651.8 KB	Display	PDB format
PDBx/mmJSON format	9dy7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dy/9dy7 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/9dy7	HTTPS FTP

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Related structure data

Related structure data	8v2kC 8v4aC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tryptophanase (with internal aldimine)

B: Tryptophanase

C: Tryptophanase (with internal aldimine)

D: Tryptophanase

hetero molecules

212 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	111.330, 113.676, 149.414
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab

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Protein , 2 types, 4 molecules ACBD

#1: Protein	Tryptophanase (with internal aldimine) / L-tryptophan indole-lyase / TNase Mass: 52655.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: tnaA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28796, tryptophanase
#2: Protein	Tryptophanase / L-tryptophan indole-lyase / TNase Mass: 52427.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: tnaA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28796, tryptophanase

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Non-polymers , 7 types, 1224 molecules

#3: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-ESC / 2-AMINO-4-ETHYL SULFANYL BUTYRIC ACID Type: L-peptide linking / Mass: 163.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₂S / Comment: antagonist*YM
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical	ChemComp-YAR / (2E)-4-(ethylsulfanyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}butanoic acid Mass: 392.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₁N₂O₇PS
#8: Chemical	ChemComp-YAE / (E)-S-ethyl-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-homocysteine Mass: 392.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₁N₂O₇PS
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1210 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M potassium phosphate, pH 8.0, 1 mM DTT, 0.1 mM PLP, 0.2 M KCl, 22% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.76→52.16 Å / Num. obs: 157262 / % possible obs: 99.89 % / Redundancy: 7.6 % / CC_1/2: 0.997 / Net I/σ(I): 6.69
Reflection shell	Resolution: 1.76→1.8 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 0.77 / Num. unique obs: 11101 / CC_1/2: 0.0804 / % possible all: 99.83

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
autoPROC		data reduction
Aimless		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.87→52.16 Å / SU ML: 0.2236 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1854	1999	1.27 %
R_work	0.1557	155263	-
obs	0.1561	157262	99.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 51.24 Å²

Refinement step

Cycle: LAST / Resolution: 1.87→52.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14782	0	98	1212	16092

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0056	15425
X-RAY DIFFRACTION	f_angle_d	0.7859	20862
X-RAY DIFFRACTION	f_chiral_restr	0.0511	2233
X-RAY DIFFRACTION	f_plane_restr	0.0066	2722
X-RAY DIFFRACTION	f_dihedral_angle_d	13.0375	5828

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.87-1.91	0.3258	138	0.2918	10963	X-RAY DIFFRACTION	99.83
1.91-1.96	0.3013	141	0.2695	11001	X-RAY DIFFRACTION	99.88
1.96-2.02	0.2804	145	0.2464	10968	X-RAY DIFFRACTION	99.88
2.02-2.09	0.2491	138	0.2139	10964	X-RAY DIFFRACTION	99.87
2.09-2.16	0.2458	136	0.1934	11031	X-RAY DIFFRACTION	99.88
2.16-2.25	0.1853	151	0.1745	10990	X-RAY DIFFRACTION	99.91
2.25-2.35	0.2151	141	0.1703	11052	X-RAY DIFFRACTION	99.95
2.35-2.48	0.2497	137	0.1707	11087	X-RAY DIFFRACTION	100
2.48-2.63	0.2386	148	0.1658	11040	X-RAY DIFFRACTION	100
2.63-2.83	0.1779	140	0.1573	11113	X-RAY DIFFRACTION	99.98
2.83-3.12	0.1854	142	0.1569	11087	X-RAY DIFFRACTION	99.72
3.12-3.57	0.1714	144	0.1354	11163	X-RAY DIFFRACTION	100
3.57-4.5	0.1449	145	0.1208	11241	X-RAY DIFFRACTION	100
4.5-52.16	0.1484	153	0.1349	11563	X-RAY DIFFRACTION	99.58

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.2710252459	-0.335703631492	-0.490909177392	1.56881634005	-0.487982507148	2.09683751282	0.0494749250752	-0.152356546566	0.634362514108	0.138910263337	-0.00106406872855	-0.229773584124	-0.395538292444	0.180839076831	-0.0144307275096	0.259878977264	-0.0145095282814	-0.0391319874271	0.156279372039	-0.0174364842866	0.342480301389	-38.0219519107	8.87352174582	-17.9655913748
2	4.56044953413	-0.687645174861	0.351634443935	1.79831857303	-0.197101257686	1.83583236983	-0.137074608818	-0.411640074223	0.306977572159	0.309382745953	0.0946223515994	-0.436330781338	-0.176038731111	0.281969039973	0.0304003247925	0.419892425272	0.0166398300789	-0.11030841204	0.271658585277	-0.00202696259038	0.297473974802	-25.9084025371	-12.3233767655	-3.1900203664
3	2.3744326554	-0.838567110494	0.693618851029	2.12449041428	-0.452456913928	1.95088202459	-0.0208242678942	-0.0573745076703	0.026243011604	0.253902964341	-0.00756362051416	-0.334094109803	-0.00183099322603	0.241813545939	0.0103755057523	0.25061755898	0.00979109460296	-0.0891930624546	0.196918083929	0.0152388295797	0.254391589515	-22.202436066	-14.2621857589	-12.1961457424
4	2.98410028892	-0.114601676631	-1.0789467158	2.45496769278	-0.167163376199	2.05848515204	0.1008491295	-0.311540899352	0.555898031099	0.159447770405	-0.0645498142028	-0.605061213673	-0.241786358897	0.556625071549	-0.0169937533314	0.194805538168	-0.0538506640153	-0.101622602289	0.317619441205	0.00687774887486	0.39352077544	-24.4940193685	6.39066172289	-18.7176074086
5	3.6360265106	2.14907322672	0.0536006128592	5.97407941773	1.21043712447	4.62056803956	0.44412510057	-0.905284360029	1.31389808333	0.825030885654	-0.287584966444	-0.636170070234	-1.20810736189	0.830037251273	0.024886076179	0.652605704122	-0.191094312089	-0.132168347162	0.781585860659	-0.25999916316	1.20663769673	-18.1617925418	21.4645318986	-9.53990044047
6	1.9365647511	0.784182703182	-1.03127056184	1.78310365169	-1.04961483078	1.26733902881	-0.200867216956	-0.279203996997	-0.209238466819	0.211565546163	0.152888234286	0.0911424061212	0.0490725537678	-0.0602082873119	0.0229708805591	0.311497573872	0.0682312616492	0.0447028717816	0.29534037992	0.0555270820487	0.206043358181	-56.4464395301	-8.58567936919	-0.944193393448
7	2.04248404951	-0.915104461939	0.304637904416	2.4462268258	-1.09211261021	2.46147250048	-0.432799868661	-0.892864857184	0.271467530284	0.704638580555	0.477692867542	-0.324248510836	0.399372393413	0.767930924142	0.267090631051	0.74408366698	0.355084198891	-0.215913872344	0.775201453127	-0.180896008954	0.401707914519	-37.479162554	8.87903357672	11.0921744221
8	1.83226153538	0.501626085937	-0.367735703269	1.89077270833	0.344792810222	3.35391426659	-0.570955542475	-1.02827595813	0.273912924714	1.03962057347	0.594680504041	-0.0694851439319	0.682033665669	0.695053687881	0.00231553933765	0.95670813937	0.516054204502	-0.101073213616	0.824311404339	-0.178777448119	0.167714123645	-46.2495728322	7.50350457484	19.1968565063
9	3.3377957713	-0.430079674645	-0.990496986943	2.50085889335	0.0177357022173	1.04525823258	-0.218471831281	-1.06443371623	-0.240499039006	0.770786705084	0.128074750648	0.234932961118	-0.0351568350292	0.298860020424	-0.0866349100244	0.513691592451	0.156557703861	0.0596080321533	0.647891887796	0.141590218095	0.104190465521	-56.9611657429	-8.87639883125	13.0988277089
10	5.84663471188	-1.75638352216	0.239730603758	1.31499359013	1.19733601159	2.11500665426	-0.4756003461	-0.470790970943	-1.31529554787	1.19335181525	0.106213128078	-0.0382983324332	0.474415484935	1.08950189575	0.2423208527	0.824082163025	0.284548296498	0.186962269138	1.23930639573	0.554822784028	0.568350022539	-50.2519995331	-26.0587102811	15.8875551696
11	1.7231486708	-0.360872793076	-0.197091943108	1.20378165635	-0.486403597214	1.55820082893	-0.134896781733	0.0896672182734	-0.0674892774244	-0.0922342761068	0.0351320988729	0.0574295711514	0.180695249834	-0.0782662603182	0.0970778200893	0.235682483929	-0.0262842702398	-0.0274146348205	0.148857316975	0.0364034457073	0.204878085674	-55.2182161788	5.44713426452	-31.1220125334
12	3.87678331559	0.248683804198	0.853030888016	3.08827766	-3.01994574809	6.03036946628	0.0487541142256	0.328751271871	-0.148465295968	-0.736328755018	0.22020562038	0.275135976828	0.54680655173	-0.370189448452	-0.22648468264	0.516164810985	-0.0126122458753	-0.142208800746	0.352919463864	0.0580136628491	0.397062518555	-73.6108624549	17.3107662805	-47.4905086241
13	1.54108249937	-1.12943373974	0.857000134967	1.82085496474	-0.645414441343	0.987489464623	-0.0680299414296	0.14095597267	0.232507599831	-0.122186003435	-0.00643728858167	0.015734623151	-0.0767001485532	-0.0501670058312	0.0377145653019	0.285341453815	-0.00454187887545	-0.0572715540041	0.203670996057	0.0674778864064	0.284194861632	-60.9554559628	21.3227328557	-39.5675105752
14	2.18726016514	-0.0965507053581	-0.8186973605	1.87946766388	-0.149115802427	2.93903283146	-0.0586186866741	0.819170246882	-0.175021504022	-0.726598648229	-0.129998153978	0.0622719073867	0.41486232121	-0.383245658527	0.122541364316	0.520269270608	0.0183616511904	-0.0231342654847	0.50184069056	-0.00448995469919	0.218281473602	-51.6967933794	0.45242764575	-53.0193091411
15	2.00004047789	4.56898324134	9.40601784877	7.18264382962	3.6552853375	7.98221694865	-0.656863619919	2.24308331082	-0.228656145335	0.368136371604	1.18649870043	-0.212531459266	0.874456772706	0.339771276579	-0.449417320253	1.94050732419	0.210677316606	-0.13896318135	1.24042214835	-0.614436385355	2.35051261174	-51.0966629256	-16.0587894464	-64.6870641779
16	1.84994265283	0.418957944502	-1.10949688184	1.71154340158	-0.361604752253	1.97773168028	0.0929719261111	-0.111434134786	0.335127893997	0.360883035328	0.113983698427	0.50330379935	-0.299201214856	-0.316741471021	-0.0660246659468	0.312946163117	0.0789708422724	0.0795275912941	0.283755233113	0.0642915325538	0.383758168262	-71.198463188	4.77715226075	-10.4250993495
17	5.06220957229	-0.971815893817	0.920194739494	2.49458254871	-0.938001646282	1.82981029541	0.00675578708145	0.319078109573	0.108845846876	-0.453993160536	0.326390931636	0.949151600283	0.144526685927	-0.498824831736	-0.195566320355	0.442219334234	-0.0518478076042	-0.222204965249	0.383860213072	0.162154145019	0.598374297721	-78.5045192722	-8.05885279348	-35.4844243794
18	2.10075856836	0.558152324885	0.076051242273	2.90551336386	0.525097821833	2.40736915031	-0.0489689466316	0.125987048661	0.206611083574	-0.327601398258	0.246088742727	1.25628727026	0.102878499691	-0.764956803963	0.0371585706363	0.277993970769	-0.0914104459231	-0.189518771506	0.510824306771	0.228889840028	0.856627570517	-86.1640221498	-12.0862292865	-27.1665176258
19	1.6247469754	-0.0243852565188	-0.4491252088	2.21081785125	-0.565998677237	2.52314740465	0.000673265219472	-0.0060572340217	0.127997548164	0.193359908554	0.330247689929	0.867703401201	-0.112801663085	-0.924385183631	0.0974366033116	0.212337492367	0.0787888688721	0.0839154037578	0.562454068276	0.213137903941	0.62341242627	-84.7333176387	1.01112017405	-12.7202571566
20	3.46285932087	0.451678205106	0.609276689569	0.852042173568	0.303312401082	0.255692472062	-0.0863676713737	0.405148533072	0.843708790945	0.46404415948	0.0535823384611	0.645563698905	-0.829570201539	-0.603278783013	0.179684522719	0.665762558471	0.2938065063	0.275996360547	0.83136297093	0.225440418012	0.910437779942	-89.2549407393	13.5996475749	-8.05617615561

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 2 through 75 )	A	A	2 - 75	1 - 74
2	2	chain 'A' and (resid 76 through 155 )	A	A	76 - 155	75 - 154
3	3	chain 'A' and (resid 156 through 295 )	A	A	156 - 295	155 - 294
4	4	chain 'A' and (resid 296 through 437 )	A	A	296 - 437	295 - 436
5	5	chain 'A' and (resid 438 through 467 )	A	A	438 - 467	437 - 466
6	6	chain 'B' and (resid 2 through 75 )	B	B	2 - 75	1 - 74
7	7	chain 'B' and (resid 76 through 132 )	B	B	76 - 132	75 - 131
8	8	chain 'B' and (resid 133 through 295 )	B	B	133 - 295	132 - 294
9	9	chain 'B' and (resid 296 through 437 )	B	B	296 - 437	295 - 436
10	10	chain 'B' and (resid 438 through 467 )	B	B	438 - 467	437 - 466
11	11	chain 'C' and (resid 2 through 99 )	C	C	2 - 99	1 - 98
12	12	chain 'C' and (resid 100 through 155 )	C	C	100 - 155	99 - 154
13	13	chain 'C' and (resid 156 through 342 )	C	C	156 - 342	155 - 341
14	14	chain 'C' and (resid 343 through 466 )	C	C	343 - 466	342 - 465
15	15	chain 'C' and (resid 467 through 467 )	C	C	467	466
16	16	chain 'D' and (resid 2 through 75 )	D	D	2 - 75	1 - 74
17	17	chain 'D' and (resid 76 through 132 )	D	D	76 - 132	75 - 131
18	18	chain 'D' and (resid 133 through 295 )	D	D	133 - 295	132 - 294
19	19	chain 'D' and (resid 296 through 423 )	D	D	296 - 423	295 - 422
20	20	chain 'D' and (resid 424 through 467 )	D	D	424 - 467	423 - 466

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Protein , 2 types, 4 molecules ACBD

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